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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Involved in the succinylase branch of the diaminopimelate biosynthesis.1 Publication

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei15 – 151SubstrateBy similarity
Binding sitei48 – 481SubstrateBy similarity
Binding sitei74 – 741SubstrateBy similarity
Active sitei83 – 831Proton donor/acceptorBy similarity
Binding sitei159 – 1591SubstrateBy similarity
Sitei161 – 1611Important for catalytic activityBy similarity
Binding sitei194 – 1941SubstrateBy similarity
Sitei212 – 2121Important for catalytic activityBy similarity
Active sitei221 – 2211Proton donor/acceptorBy similarity

GO - Molecular functioni

  1. diaminopimelate epimerase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimerase (EC:5.1.1.7)
Short name:
DAP epimerase
Gene namesi
Name:dapF
Ordered Locus Names:Cgl1943, cg2129
OrganismiCorynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Taxonomic identifieri196627 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeCorynebacteriaceaeCorynebacterium
ProteomesiUP000001009 Componenti: Chromosome UP000000582 Componenti: Chromosome

Subcellular locationi

  1. Cytoplasm By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 277277Diaminopimelate epimerasePRO_0000149837Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi83 ↔ 221

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi196627.cg2129.

Structurei

3D structure databases

ProteinModelPortaliQ8NP73.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni83 – 853Substrate bindingBy similarity
Regioni212 – 2132Substrate bindingBy similarity
Regioni222 – 2232Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.Curated

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8NP73-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNLTIPFAKG HATENDFIII PDEDARLDLT PEMVVTLCDR RAGIGADGIL
60 70 80 90 100
RVVKAADVEG STVDPSLWFM DYRNADGSLA EMCGNGVRLF AHWLYSRGLV
110 120 130 140 150
DNTSFDIGTR AGVRHVDILQ ADQHSAQVRV DMGIPDVTGL STCDINGQVF
160 170 180 190 200
AGLGVDMGNP HLACVVPGLS ASALADMELR APTFDQEFFP HGVNVEIVTE
210 220 230 240 250
LEDDAVSMRV WERGVGETRS CGTGTVAAAC AALADAGLGE GTVKVCVPGG
260 270
EVEVQIFDDG STLTGPSAII ALGEVQI
Length:277
Mass (Da):29,203
Last modified:October 25, 2002 - v1
Checksum:i41458032D8C7E9DF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000036 Genomic DNA. Translation: BAB99336.1.
BX927153 Genomic DNA. Translation: CAF20284.1.
RefSeqiNP_601150.1. NC_003450.3.
YP_226185.1. NC_006958.1.

Genome annotation databases

EnsemblBacteriaiBAB99336; BAB99336; BAB99336.
GeneIDi1019900.
KEGGicgb:cg2129.
cgl:NCgl1868.
PATRICi21495890. VBICorGlu203724_1881.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000036 Genomic DNA. Translation: BAB99336.1.
BX927153 Genomic DNA. Translation: CAF20284.1.
RefSeqiNP_601150.1. NC_003450.3.
YP_226185.1. NC_006958.1.

3D structure databases

ProteinModelPortaliQ8NP73.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi196627.cg2129.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB99336; BAB99336; BAB99336.
GeneIDi1019900.
KEGGicgb:cg2129.
cgl:NCgl1868.
PATRICi21495890. VBICorGlu203724_1881.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The Corynebacterium glutamicum genome: features and impacts on biotechnological processes."
    Ikeda M., Nakagawa S.
    Appl. Microbiol. Biotechnol. 62:99-109(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
  3. "Identification and characterization of the last two unknown genes, dapC and dapF, in the succinylase branch of the L-lysine biosynthesis of Corynebacterium glutamicum."
    Hartmann M., Tauch A., Eggeling L., Bathe B., Mockel B., Puhler A., Kalinowski J.
    J. Biotechnol. 104:199-211(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.

Entry informationi

Entry nameiDAPF_CORGL
AccessioniPrimary (citable) accession number: Q8NP73
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 25, 2002
Last sequence update: October 25, 2002
Last modified: April 1, 2015
This is version 79 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.